Department of Homeland Security Appropriations Act, 2013 - Makes appropriations for the Department of Homeland Security (DHS) for FY2013. Title I: Departmental Management and Operations - Makes appropriations for: (1) the Office of the Secretary and executive management, (2) the Office of the Under Secretary for Management, (3) the Office of the Chief Financial Officer, (4) the Office of the Chief Information Officer, (5) intelligence analysis and operations activities, and (6) the Office of the Inspector General. Title II: Security, Enforcement, and Investigations - Makes appropriations for: (1) U.S. Customs and Border Protection (CBP), including for border security fencing, infrastructure, and technology; (2) U.S. Immigration and Customs Enforcement (ICE), including to reimburse other federal agencies for the costs associated with the care, maintenance, and repatriation of smuggled aliens unlawfully present in the United States, to identify and remove from the United States aliens convicted of a crime once they are judged deportable, and for detention and removal operations, including alternatives to detention; (3) the Transportation Security Administration (TSA), including for aviation security (including explosives detection systems), surface transportation security, screening programs of the Office of Transportation Threat Assessment and Credentialing, transportation security support and intelligence, and the Federal Air Marshals; (4) the Coast Guard, including funding derived from the Oil Spill Liability Trust Fund for prevention, removal, and enforcement related to oil discharges and funding for environmental compliance and restoration; and (5) the U.S. Secret Service. Title III: Protection, Preparedness, Response, and Recovery - Makes appropriations for FY2013 for: (1) the Office of the Under Secretary for the National Protection and Programs Directorate, including for the Federal Protective Service and the Office of Biometric Identity Management; (2) the Office of Health Affairs, including for BioWatch operations; and (3) the Federal Emergency Management Agency (FEMA), including for grants for state and local programs, firefighter assistance grants, emergency management performance grants, the U.S. Fire Administration, disaster relief, the disaster assistance direct loan program account, the flood hazard mapping and risk analysis program, the National Flood Insurance Fund, the predisaster mitigation grant program, and the emergency food and shelter program. Title IV: Research and Development, Training, and Services - Makes appropriations for FY2013 for: (1) U.S. Citizenship and Immigration Services (CIS), including for the E-Verify program; (2) the Federal Law Enforcement Training Center; (3) the Office of the Under Secretary for Science and Technology; and (4) the Domestic Nuclear Detection Office. Title V: General Provisions - (Sec. 501) Sets forth limitations and prohibitions on the availability, use, reprogramming, or transfer of funds for specified programs and activities under this Act. (Sec. 513) Prohibits the use of funds available in this Act to amend the oath of allegiance required under the Immigration and Nationality Act. (Sec. 522) Prohibits the use of funds by CIS to grant an immigration benefit unless the results of required background checks have been received and do not preclude granting the benefit. (Sec. 526) Prohibits the use of funds for CBP to prevent an individual from importing a prescription drug from Canada if: (1) such individual is not in the business of importing a prescription drug; and (2) such drug complies with specified provisions of the Federal Food, Drug, and Cosmetic Act and is not a controlled substance or a biological product. Makes this section applicable only to individuals transporting on their person a personal-use quantity of the prescription drug, not exceeding a 90-day supply. (Sec. 528) Prohibits the use of funds made available in this Act: (1) for planning, testing, piloting, or developing a national identification card; (2) to transfer, release, or assist in the transfer or release to or within the United States, its territories, or possessions, of Khalid Sheikh Mohammed or any other detainee who is not a U.S. citizen or a member of the U.S. Armed Forces, or who is or was held on or after June 24, 2009, at the U.S. Naval Station, Guantanamo Bay, Cuba, by the Department of Defense (DOD); or (3) to employ unauthorized aliens. (Sec. 537) Requires any company that collects or retains personal information directly from any individual who participates in TSA's Registered Traveler or successor program to safeguard and dispose of such information in accordance with specified requirements. (Sec. 539) Requires the TSA Administrator to: (1) submit to the House and Senate Appropriations Committees a report that either certifies that the requirement for screening all air cargo on passenger aircraft by the deadline has been met or includes a strategy to comply with such requirements, and (2) continue to submit such reports every 90 days until the Administrator has achieved screening of 100% of such air cargo. (Sec. 543) Provides that any sale or collocation of federally owned detention facilities shall not result in the maintenance of fewer than 34,000 ICE detention beds. (Sec. 544) Prohibits funds made available under this Act or any prior appropriations Act from being provided to the Association of Community Organizations for Reform Now (ACORN) or any of its affiliates, subsidiaries, or allied organizations. (Sec. 546) Requires the DHS Secretary to ensure enforcement of immigration laws. (Sec. 554) Prohibits funds made available under this Act from being used by a federal law enforcement officer to facilitate the transfer of an operable firearm to an individual if the officer knows or suspects that the individual is an agent of a drug cartel unless U.S. law enforcement personnel continuously monitor or control the firearm at all times. (Sec. 560) Rescinds various amounts from specified agencies, including FEMA, the Coast Guard, and CBP. (Sec. 564) Repeals a provision directing TSA to retain any unclaimed money recovered at airport security checkpoints until expended for the purpose of providing civil aviation security. (Sec. 566) Prohibits funds appropriated by this Act for ICE from: (1) being available to pay for an abortion, except where the mother's life would be endangered if the fetus were carried to term, or in the case of rape or incest; or (2) being used to require any person to perform, or facilitate the performance of, an abortion. (Sec. 571) Prohibits the use of funds: (1) to implement or enforce the DHS rule entitled "Provisional Unlawful Presence Waivers of Inadmissibility for Certain Immediate Relatives," published on April 2, 2012; (2) for the position of Public Advocate within ICE; (3) for the purchase, operation, or maintenance of armed unmanned aerial vehicles; (4) to enforce Executive Order 13166 (directing agencies to expand access to services for those with limited English proficiency); (5) to finalize, implement, administer, or enforce the "Morton Memos" (regarding the civil immigration enforcement priorities of ICE and the use of prosecutorial discretion in removal cases involving the victims and witnesses of crime); or (6) to terminate an existing agreement regarding immigration enforcement powers delegated to state and local authorities.